New mlr json-parse -k flag (#1291)

* New `mlr json-parse -k` flag

* docs / make-dev artifacts

* Add unit-test files for the feature

* codespell

docs/src/data-diving-examples.md

@@ -160,11 +160,11 @@ CITRUS COUNTY 1332.9 79974.9 483785.1
 <b> stats2 -a corr,linreg-ols,r2 -f tiv_2011,tiv_2012</b>
 </pre>
 <pre class="pre-non-highlight-in-pair">
-tiv_2011_tiv_2012_corr 0.9730497632351692
-tiv_2011_tiv_2012_ols_m 0.9835583980337723
-tiv_2011_tiv_2012_ols_b 433854.6428968317
+tiv_2011_tiv_2012_corr 0.9730497632351701
+tiv_2011_tiv_2012_ols_m 0.9835583980337732
+tiv_2011_tiv_2012_ols_b 433854.6428968301
 tiv_2011_tiv_2012_ols_n 36634
-tiv_2011_tiv_2012_r2 0.9468258417320189
+tiv_2011_tiv_2012_r2 0.9468258417320204
 </pre>
 
 <pre class="pre-highlight-in-pair">
@@ -322,7 +322,7 @@ Look at bivariate stats by color and shape. In particular, `u,v` pairwise correl
 </pre>
 <pre class="pre-non-highlight-in-pair">
  u_v_corr w_x_corr
-0.1334180491027861 -0.011319841199866178
+0.1334180491027861 -0.011319841199852926
 </pre>
 
 <pre class="pre-highlight-in-pair">
@@ -332,22 +332,22 @@ Look at bivariate stats by color and shape. In particular, `u,v` pairwise correl
 </pre>
 <pre class="pre-non-highlight-in-pair">
  color shape u_v_corr w_x_corr
- red circle 0.9807984401887236 -0.01856553658708754
-orange square 0.17685855992752927 -0.07104431573806054
- green circle 0.05764419437577255  0.01179572988801509
- red square 0.05574477124893523 -0.0006801456507510942
-yellow triangle 0.04457273771962798 0.024604310103081825
-yellow square 0.04379172927296089 -0.04462197201631237
-purple circle 0.03587354936895086  0.1341133954140899
- blue square 0.03241153095761164 -0.053507648119643196
- blue triangle 0.015356427073158766 -0.0006089997461435399
-orange circle 0.010518953877704048 -0.16279397329279383
- red triangle 0.00809782571528034 0.012486621357942596
-purple triangle 0.005155190909099334 -0.045057909256220656
-purple square -0.025680276963377404  0.05769429647930396
- green square  -0.0257760734502851 -0.003265173252087127
-orange triangle -0.030456661186085785  -0.1318699981926352
-yellow circle -0.06477331572781474 0.07369449819706045
- blue circle -0.10234761901929677 -0.030528539069837757
- green triangle -0.10901825107358765 -0.04848782060162929
+ red circle 0.9807984401887242 -0.018565536587084836
+orange square 0.17685855992752933 -0.07104431573805543
+ green circle 0.05764419437577257 0.011795729888018455
+ red square  0.0557447712489348 -0.0006801456507506415
+yellow triangle  0.0445727377196281 0.024604310103079844
+yellow square  0.0437917292729612 -0.044621972016306265
+purple circle 0.03587354936895115 0.13411339541407613
+ blue square 0.03241153095761152 -0.05350764811965621
+ blue triangle 0.015356427073158612 -0.0006089997461408209
+orange circle 0.010518953877704181  -0.1627939732927932
+ red triangle 0.00809782571528054  0.01248662135795501
+purple triangle 0.005155190909099739 -0.04505790925621933
+purple square  -0.02568027696337717 0.057694296479293694
+ green square -0.025776073450284875 -0.0032651732520739014
+orange triangle -0.030456661186085584 -0.13186999819263814
+yellow circle -0.06477331572781515  0.0736944981970553
+ blue circle  -0.1023476190192966 -0.030528539069839333
+ green triangle -0.10901825107358747 -0.04848782060162855
 </pre>

docs/src/manpage.md

@@ -1269,6 +1269,8 @@ MILLER(1) MILLER(1)
  Tries to convert string field values to parsed JSON, e.g. "[1,2,3]" -> [1,2,3].
  Options:
  -f {...} Comma-separated list of field names to json-parse (default all).
+ -k If supplied, then on parse fail for any cell, keep the (unparsable)
+ input value for the cell.
  -h|--help Show this message.
 
  1mjson-stringify0m
@@ -3357,5 +3359,5 @@ MILLER(1) MILLER(1)
 
 
 
- 2023-04-20 MILLER(1)
+ 2023-05-13 MILLER(1)
 </pre>

docs/src/manpage.txt

@@ -1248,6 +1248,8 @@ MILLER(1) MILLER(1)
  Tries to convert string field values to parsed JSON, e.g. "[1,2,3]" -> [1,2,3].
  Options:
  -f {...} Comma-separated list of field names to json-parse (default all).
+ -k If supplied, then on parse fail for any cell, keep the (unparsable)
+ input value for the cell.
  -h|--help Show this message.
 
  1mjson-stringify0m
@@ -3336,4 +3338,4 @@ MILLER(1) MILLER(1)
 
 
 
- 2023-04-20 MILLER(1)
+ 2023-05-13 MILLER(1)

docs/src/reference-verbs.md

@@ -1792,6 +1792,8 @@ Usage: mlr json-parse [options]
 Tries to convert string field values to parsed JSON, e.g. "[1,2,3]" -> [1,2,3].
 Options:
 -f {...} Comma-separated list of field names to json-parse (default all).
+-k If supplied, then on parse fail for any cell, keep the (unparsable)
+ input value for the cell.
 -h|--help Show this message.
 </pre>
 
@@ -3275,14 +3277,14 @@ fields, optionally categorized by one or more fields.
 <b> data/medium</b>
 </pre>
 <pre class="pre-non-highlight-in-pair">
-x_y_cov 0.000042574820827444476
-x_y_corr 0.0005042001844467462
-y_y_cov 0.08461122467974003
+x_y_cov 0.00004257482082749404
+x_y_corr 0.0005042001844473328
+y_y_cov 0.08461122467974005
 y_y_corr 1
-x2_xy_cov 0.04188382281779374
-x2_xy_corr 0.630174342037994
-x2_y2_cov -0.00030953725962542085
-x2_y2_corr -0.0034249088761121966
+x2_xy_cov 0.041883822817793716
+x2_xy_corr 0.6301743420379936
+x2_y2_cov -0.0003095372596253918
+x2_y2_corr -0.003424908876111875
 </pre>
 
 <pre class="pre-highlight-in-pair">
@@ -3291,12 +3293,12 @@ x2_y2_corr -0.0034249088761121966
 <b> data/medium</b>
 </pre>
 <pre class="pre-non-highlight-in-pair">
-a x_y_ols_m x_y_ols_b  x_y_ols_n x_y_r2 y_y_ols_m y_y_ols_b y_y_ols_n y_y_r2 xy_y2_ols_m xy_y2_ols_b xy_y2_ols_n xy_y2_r2
-pan 0.01702551273681908 0.5004028922897639 2081 0.00028691820445814767 1 0 2081 1 0.8781320866715662 0.11908230147563566 2081 0.41749827377311266
-eks 0.0407804923685586  0.48140207967651016 1965 0.0016461239223448587 1 0 1965 1 0.8978728611690183 0.10734054433612333 1965 0.45563223864254526
-wye -0.03915349075204814 0.5255096523974456 1966 0.0015051268704373607 1 0 1966 1 0.8538317334220835 0.1267454301662969 1966 0.38991721818599295
-zee 0.0027812364960399147 0.5043070448033061  2047 0.000007751652858786137 1 0 2047 1 0.8524439912011013 0.12401684308018937 2047 0.39356598090006495
-hat -0.018620577041095078 0.5179005397264935 1941 0.0003520036646055585 1 0 1941 1 0.8412305086345014 0.13557328318623216 1941 0.3687944261732265
+a x_y_ols_m x_y_ols_b x_y_ols_n x_y_r2 y_y_ols_m y_y_ols_b  y_y_ols_n y_y_r2 xy_y2_ols_m xy_y2_ols_b xy_y2_ols_n xy_y2_r2
+pan 0.017025512736819345 0.500402892289764 2081 0.00028691820445815624 1 -0.00000000000000002890430283104539 2081 1 0.8781320866715664 0.11908230147563569 2081 0.4174982737731127
+eks 0.04078049236855813 0.4814020796765104 1965 0.0016461239223448218 1 0.00000000000000017862676354313703 1965 1 0.897872861169018 0.1073405443361234 1965 0.4556322386425451
+wye -0.03915349075204785 0.5255096523974457 1966 0.0015051268704373377 1 0.00000000000000004464425401127647 1966 1 0.8538317334220837 0.1267454301662969 1966 0.3899172181859931
+zee 0.0027812364960401333 0.5043070448033061 2047 0.000007751652858787357 1 0.00000000000000004819404567023685 2047 1 0.8524439912011011 0.12401684308018947 2047 0.39356598090006495
+hat -0.018620577041095272 0.5179005397264937 1941 0.00035200366460556604 1 -0.00000000000000003400445761787692 1941 1 0.8412305086345017 0.13557328318623207 1941 0.3687944261732266
 </pre>
 
 Here's an example simple line-fit. The `x` and `y`
@@ -3382,11 +3384,11 @@ upsec_count_pca_quality 0.9999590846136102
 donesec 92.33051350964094
 
 color purple
-upsec_count_pca_m -39.03009744795354
-upsec_count_pca_b 979.9883413064914
+upsec_count_pca_m -39.030097447953594
+upsec_count_pca_b 979.9883413064917
 upsec_count_pca_n 21
 upsec_count_pca_quality 0.9999908956206317
-donesec 25.10852919630297
+donesec 25.108529196302943
 </pre>
 
 ## step
@@ -3614,9 +3616,9 @@ distinct_count 5 5 10000 10000 10000
 mode pan wye 1 0.3467901443380824 0.7268028627434533
 sum 0 0 50005000 4986.019681679581 5062.057444929905
 mean - - 5000.5 0.49860196816795804 0.5062057444929905
-stddev - - 2886.8956799071675 0.2902925151144007  0.290880086426933
-var - - 8334166.666666667 0.08426974433144456 0.08461122467974003
-skewness - - 0 -0.0006899591185521965 -0.017849760120133784
+stddev - - 2886.8956799071675 0.29029251511440074 0.2908800864269331
+var - - 8334166.666666667 0.08426974433144457 0.08461122467974005
+skewness - - 0 -0.0006899591185517494 -0.01784976012013298
 minlen 3 3 1 15 13
 maxlen 3 3 5 22 22
 min eks eks 1 0.00004509679127584487 0.00008818962627266114

docs/src/two-pass-algorithms.md

@@ -598,8 +598,8 @@ hat pan 0.4643355557376876
 x_count 10000
 x_sum 4986.019681679581
 x_mean 0.49860196816795804
-x_var 0.08426974433144456
-x_stddev 0.2902925151144007
+x_var 0.08426974433144457
+x_stddev 0.29029251511440074
 </pre>
 
 <pre class="pre-highlight-in-pair">

internal/pkg/mlrval/mlrmap_json.go

@@ -169,6 +169,14 @@ func (entry *MlrmapEntry) JSONParseInPlace() {
  }
 }
 
+func (entry *MlrmapEntry) JSONTryParseInPlace() {
+ input := entry.Value.String()
+ pmv, err := TryUnmarshalJSON([]byte(input))
+ if err == nil {
+ entry.Value = pmv
+ }
+}
+
 // StringifyValuesRecursively is nominally for the `--jvquoteall` flag.
 func (mlrmap *Mlrmap) StringifyValuesRecursively() {
  for pe := mlrmap.Head; pe != nil; pe = pe.Next {

internal/pkg/mlrval/mlrval_json.go

@@ -114,6 +114,16 @@ func (mv *Mlrval) UnmarshalJSON(inputBytes []byte) error {
  return nil
 }
 
+// ----------------------------------------------------------------
+func TryUnmarshalJSON(inputBytes []byte) (pmv *Mlrval, err error) {
+ decoder := json.NewDecoder(bytes.NewReader(inputBytes))
+ pmv, eof, err := MlrvalDecodeFromJSON(decoder)
+ if eof {
+ err = fmt.Errorf("mlr: JSON parser: unexpected premature EOF.")
+ }
+ return pmv, err
+}
+
 // ----------------------------------------------------------------
 func MlrvalDecodeFromJSON(decoder *json.Decoder) (
  mlrval *Mlrval,

internal/pkg/transformers/json_parse.go

@@ -31,6 +31,8 @@ func transformerJSONParseUsage(
  )
  fmt.Fprintf(o, "Options:\n")
  fmt.Fprintf(o, "-f {...} Comma-separated list of field names to json-parse (default all).\n")
+ fmt.Fprintf(o, "-k If supplied, then on parse fail for any cell, keep the (unparsable)\n")
+ fmt.Fprintf(o, " input value for the cell.\n")
  fmt.Fprintf(o, "-h|--help Show this message.\n")
 }
 
@@ -46,6 +48,7 @@ func transformerJSONParseParseCLI(
  argi := *pargi
  verb := args[argi]
  argi++
+ keepFailed := false
 
  var fieldNames []string = nil
 
@@ -66,6 +69,9 @@ func transformerJSONParseParseCLI(
  } else if opt == "-f" {
  fieldNames = cli.VerbGetStringArrayArgOrDie(verb, opt, args, &argi, argc)
 
+ } else if opt == "-k" {
+ keepFailed = true
+
  } else {
  transformerJSONParseUsage(os.Stderr)
  os.Exit(1)
@@ -79,6 +85,7 @@ func transformerJSONParseParseCLI(
 
  transformer, err := NewTransformerJSONParse(
  fieldNames,
+ keepFailed,
  )
  if err != nil {
  fmt.Fprintln(os.Stderr, err)
@@ -92,13 +99,15 @@ func transformerJSONParseParseCLI(
 type TransformerJSONParse struct {
  // input
  fieldNameSet map[string]bool
+ keepFailed bool
 
  // state
  recordTransformerFunc RecordTransformerFunc
 }
 
 func NewTransformerJSONParse(
  fieldNames []string,
+ keepFailed bool,
 ) (*TransformerJSONParse, error) {
  var fieldNameSet map[string]bool = nil
  if fieldNames != nil {
@@ -107,6 +116,7 @@ func NewTransformerJSONParse(
 
  retval := &TransformerJSONParse{
  fieldNameSet: fieldNameSet,
+ keepFailed: keepFailed,
  }
 
  retval.recordTransformerFunc = retval.jsonParseAll
@@ -139,7 +149,11 @@ func (tr *TransformerJSONParse) jsonParseAll(
  if !inrecAndContext.EndOfStream {
  inrec := inrecAndContext.Record
  for pe := inrec.Head; pe != nil; pe = pe.Next {
- pe.JSONParseInPlace()
+ if tr.keepFailed {
+ pe.JSONTryParseInPlace()
+ } else {
+ pe.JSONParseInPlace()
+ }
  }
  outputRecordsAndContexts.PushBack(inrecAndContext)
  } else {
@@ -158,7 +172,11 @@ func (tr *TransformerJSONParse) jsonParseSome(
  inrec := inrecAndContext.Record
  for pe := inrec.Head; pe != nil; pe = pe.Next {
  if tr.fieldNameSet[pe.Key] {
- pe.JSONParseInPlace()
+ if tr.keepFailed {
+ pe.JSONTryParseInPlace()
+ } else {
+ pe.JSONParseInPlace()
+ }
  }
  }
  outputRecordsAndContexts.PushBack(inrecAndContext)

man/manpage.txt

@@ -1248,6 +1248,8 @@ MILLER(1) MILLER(1)
  Tries to convert string field values to parsed JSON, e.g. "[1,2,3]" -> [1,2,3].
  Options:
  -f {...} Comma-separated list of field names to json-parse (default all).
+ -k If supplied, then on parse fail for any cell, keep the (unparsable)
+ input value for the cell.
  -h|--help Show this message.
 
  1mjson-stringify0m
@@ -3336,4 +3338,4 @@ MILLER(1) MILLER(1)
 
 
 
- 2023-04-20 MILLER(1)
+ 2023-05-13 MILLER(1)

man/mlr.1

@@ -2,12 +2,12 @@
 .\" Title: mlr
 .\" Author: [see the "AUTHOR" section]
 .\" Generator: ./mkman.rb
-.\" Date: 2023-04-20
+.\" Date: 2023-05-13
 .\" Manual: \ \&
 .\" Source: \ \&
 .\" Language: English
 .\"
-.TH "MILLER" "1" "2023-04-20" "\ \&" "\ \&"
+.TH "MILLER" "1" "2023-05-13" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Portability definitions
 .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -1575,6 +1575,8 @@ Usage: mlr json-parse [options]
 Tries to convert string field values to parsed JSON, e.g. "[1,2,3]" -> [1,2,3].
 Options:
 -f {...} Comma-separated list of field names to json-parse (default all).
+-k If supplied, then on parse fail for any cell, keep the (unparsable)
+ input value for the cell.
 -h|--help Show this message.
 .fi
 .if n \{\

test/cases/cli-help/0001/expout

@@ -415,6 +415,8 @@ Usage: mlr json-parse [options]
 Tries to convert string field values to parsed JSON, e.g. "[1,2,3]" -> [1,2,3].
 Options:
 -f {...} Comma-separated list of field names to json-parse (default all).
+-k If supplied, then on parse fail for any cell, keep the (unparsable)
+ input value for the cell.
 -h|--help Show this message.
 
 ================================================================

test/cases/verb-json-parse-json-stringify/0027-k/cmd

@@ -0,0 +1 @@
+mlr --c2j json-parse test/input/json-parse-with-error.csv

test/cases/verb-json-parse-json-stringify/0027-k/expout

@@ -0,0 +1,19 @@
+[
+{
+ "foo": "ts",
+ "bar": "some value",
+ "baz": 10
+},
+{
+ "foo": "ts",
+ "bar": (error),
+ "baz": 10
+},
+{
+ "foo": "ts",
+ "bar": {
+ "key": "val"
+ },
+ "baz": 10
+}
+]

test/cases/verb-json-parse-json-stringify/0028-k/cmd

@@ -0,0 +1 @@
+mlr --c2j json-parse -k test/input/json-parse-with-error.csv

test/cases/verb-json-parse-json-stringify/0028-k/expout

@@ -0,0 +1,19 @@
+[
+{
+ "foo": "ts",
+ "bar": "some value",
+ "baz": 10
+},
+{
+ "foo": "ts",
+ "bar": "{key:\"val\"}",
+ "baz": 10
+},
+{
+ "foo": "ts",
+ "bar": {
+ "key": "val"
+ },
+ "baz": 10
+}
+]

test/input/json-parse-with-error.csv

@@ -0,0 +1,4 @@
+foo,bar,baz
+"""ts""","""some value""",10
+"""ts""","{key:""val""}",10
+"""ts""","{""key"":""val""}",10